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Calcium in PDB 1jap: Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)

Enzymatic activity of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)

All present enzymatic activity of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form):
3.4.24.34;

Protein crystallography data

The structure of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1jap was solved by W.Bode, P.Reinemer, R.Huber, T.Kleine, S.Schnierer, H.Tschesche, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.090, 69.370, 72.480, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / n/a

Other elements in 1jap:

The structure of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) (pdb code 1jap). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1jap:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1jap

Go back to Calcium Binding Sites List in 1jap
Calcium binding site 1 out of 2 in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca996

b:12.2
occ:1.00
O A:GLY169 2.2 17.4 1.0
O A:HOH1027 2.2 18.8 1.0
O A:ASP137 2.3 14.9 1.0
O A:GLY171 2.3 17.1 1.0
OD1 A:ASP173 2.5 17.1 1.0
O A:HOH1026 2.5 12.6 1.0
C A:GLY169 3.4 21.3 1.0
CG A:ASP173 3.4 22.1 1.0
C A:ASP137 3.5 12.4 1.0
C A:GLY171 3.5 19.8 1.0
OD2 A:ASP173 3.8 14.6 1.0
C A:ILE170 3.9 9.2 1.0
N A:GLY171 3.9 13.2 1.0
O A:ILE170 4.1 11.8 1.0
N A:ASP173 4.2 10.2 1.0
CA A:GLY171 4.2 14.0 1.0
O A:GLY167 4.3 17.1 1.0
N A:ILE170 4.3 24.2 1.0
CA A:GLY169 4.3 15.2 1.0
CA A:ASP137 4.4 15.0 1.0
N A:GLY169 4.4 18.1 1.0
CA A:ILE170 4.4 17.3 1.0
O A:ALA136 4.4 16.1 1.0
N A:ILE138 4.4 14.6 1.0
ND2 A:ASN139 4.5 19.5 1.0
N A:GLY172 4.5 10.8 1.0
O A:HOH1028 4.5 55.9 1.0
CA A:ILE138 4.6 17.4 1.0
CB A:ASP173 4.6 13.4 1.0
O A:HOH1045 4.7 21.0 1.0
C A:GLY172 4.7 15.0 1.0
CA A:GLY172 4.7 7.3 1.0
C A:GLN168 4.7 33.6 1.0
N A:ASN139 4.7 13.8 1.0
CA A:ASP173 4.8 5.9 1.0
CH2 A:TRP88 4.9 35.2 1.0

Calcium binding site 2 out of 2 in 1jap

Go back to Calcium Binding Sites List in 1jap
Calcium binding site 2 out of 2 in the Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Pro-Leu-Gly-Hydroxylamine with the Catalytic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca997

b:11.8
occ:1.00
OE2 A:GLU180 2.1 17.6 1.0
O A:ILE159 2.2 11.3 1.0
O A:GLY155 2.2 16.4 1.0
OD1 A:ASP154 2.2 14.8 1.0
O A:ASN157 2.3 15.2 1.0
OD2 A:ASP177 2.5 9.2 1.0
CD A:GLU180 3.3 8.4 1.0
C A:ILE159 3.3 9.7 1.0
CG A:ASP177 3.4 18.2 1.0
CG A:ASP154 3.4 23.8 1.0
C A:ASN157 3.4 14.4 1.0
C A:GLY155 3.5 8.4 1.0
N A:ILE159 3.8 16.4 1.0
N A:ASN157 3.9 16.7 1.0
CB A:ASP177 4.0 32.0 1.0
OD2 A:ASP154 4.0 14.8 1.0
C A:PRO156 4.0 19.2 1.0
N A:GLY155 4.0 9.8 1.0
OE1 A:GLU180 4.1 16.3 1.0
CA A:ILE159 4.1 17.2 1.0
C A:GLY158 4.1 17.1 1.0
C A:ASP154 4.2 26.1 1.0
CA A:ASN157 4.2 17.1 1.0
N A:ASP154 4.3 18.1 1.0
OD1 A:ASP177 4.3 10.8 1.0
O A:PRO156 4.3 16.0 1.0
N A:PRO156 4.4 17.2 1.0
N A:LEU160 4.4 15.1 1.0
CA A:GLY155 4.4 4.1 1.0
CG A:GLU180 4.4 11.3 1.0
N A:GLY158 4.4 6.7 1.0
CA A:PRO156 4.5 23.8 1.0
O A:ASP154 4.5 29.1 1.0
CA A:ASP154 4.5 19.4 1.0
CA A:GLY158 4.5 7.2 1.0
CB A:ILE159 4.5 19.6 1.0
CB A:ASP154 4.6 16.5 1.0
O A:GLY158 4.6 9.1 1.0
CA A:LEU160 4.6 16.2 1.0

Reference:

W.Bode, P.Reinemer, R.Huber, T.Kleine, S.Schnierer, H.Tschesche. The X-Ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited By A Substrate Analogue Reveals the Essentials For Catalysis and Specificity. Embo J. V. 13 1263 1994.
ISSN: ISSN 0261-4189
PubMed: 8137810
Page generated: Sat Dec 12 03:01:48 2020

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